Microorganisms which inhabit the soil are of substantial importance to plant scientists and the agricultural industry. Many such microorganisms have beneficial effects; for example, the roots of most legumes develop nodules which are colonized by nitrogen-fixing bacteria. Such. bacteria convert atmospheric nitrogen (N.sub.2) into other forms of nitrogen such as ammonia and urea, which plants can utilize. Such legumes usually do not require nitrogen-containing fertilizers.
However, some soil microorganisms have detrimental effects upon plants. For example, numerous types of soil fungi hinder the germination of seeds and slow the growth of seedlings. Also, various types of soil bacteria cause plant roots to shrivel, and cause abnormal plant development or plant tumors such as hairy root disease and crown gall disease.
An important concept in rhizobiology (the biology of soil, roots, etc.) relates to microbial competition. See, e.g., Cook 1983 (note: a list of references with full citations is contained after the examples). Different microbes in any given area compete with each other for nutrients and energy sources This competition leads to a continually changing balance in the population of different bacterial and fungal types. It is very difficult to accurately analyze soil microbial competition over an area that is large enough to reflect the conditions in an entire field, and it is also difficult to create accurate models of soil microbial competition under controlled conditions in a laboratory or greenhouse. The difficulty of studying soil microbial competition is greatly increased by several factors, including (a) the great difficulty in adequately differentiating between different but similar strains, species, and genera of microorganisms, and (b) the inability of a scientist to determine whether a certain culture of a microoroganism in a field descended from a different culture elsewhere in the field, (c) the ability of microorganisms to exchange genes, particularly under conditions of competitive stress. In addition, culture media developed for laboratory use is capable of culturing only a very small fraction (estimated to be less than 1%) of the microorganisms actually present in a soil sample, as indicated by direct microscopic examination; see Alexander 1977, Chapter 2. For example, nutrient broth is toxic to some types of soil microorganisms.